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| Status |
Public on Nov 29, 2019 |
| Title |
SH-SY5Y cells, DCC-IP-1 |
| Sample type |
SRA |
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| Source name |
SH-SY5Y cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: neuroblastoma cells
rip antibody: mouse-anti-DCC (BD Biosciences, 554223)
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| Growth protocol |
The cells were cultured at 37C and 5% CO2 in DMEM high glucose medium supplemented with 10% FBS
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| Extracted molecule |
total RNA |
| Extraction protocol |
The lysate of SH-SY5Y cells was incubated with magnetic Dynabeads pre-coupled with antibodies (mouse-anti-DCC (BD Biosciences, 554223); rabbit-anti-Nrp1 (Abcam, ab81321)) for 1.5 hours at 4°C. Beads were then washed 3 times and processed for RNA isolation.
Immunopurified RNAs are reverse-transcribed, and then amplified by a PCR-based method (Tang et al., Nat Methods 6, 2009).
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina bcl2fastq2 Conversion Software v2.20 was used for de-multiplexing and base-calling.
Sequence reads were aligned to the genome using Hisat2 v2.1.0
Read counts for each gene were determined using HTSeq version 0.11.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene
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| Submission date |
Aug 03, 2019 |
| Last update date |
Nov 30, 2019 |
| Contact name |
Christine E Holt |
| Organization name |
University of Cambridge
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| Department |
Department of PDN
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| Street address |
Anatomy Bldg., Downing St.
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| City |
Cambridge |
| ZIP/Postal code |
CB2 3DY |
| Country |
United Kingdom |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE135338 |
Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons |
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| Relations |
| BioSample |
SAMN12478805 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4006649_DCC-IP-1_count.txt.gz |
131.8 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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